I opened a file 1alu in pymol and ran script CenterOfMass.py. When I gave
the command com 1alu, state=1, it displays a message
AttributeError: 'module' object has no attribute 'get_legal_name'...
Iam unable to figure out why is this so.,
Hi Kanika,
I opened a file 1alu in pymol and ran script CenterOfMass.py. When I gave
the command com 1alu, state=1, it displays a message
AttributeError: 'module' object has no attribute 'get_legal_name'...
Iam unable to figure out why is this so.,
It sounds like your PyMOL is out of
version 1.1 r1
On Mon, Apr 11, 2011 at 12:04 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Kanika,
I opened a file 1alu in pymol and ran script CenterOfMass.py. When I gave
the command com 1alu, state=1, it displays a message
AttributeError: 'module' object has no
Hi Kanika,
That version is too old, hence the missing command. It's probably
wise to upgrade.
Cheers,
-- Jason
On Mon, Apr 11, 2011 at 2:50 AM, kanika sharma ksharma...@gmail.com wrote:
version 1.1 r1
On Mon, Apr 11, 2011 at 12:04 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Kanika, Jason,
cmd.get_legal_name is only called in 'com' if no object name is given.
The quickest workaround thus is to provide an object name for the
'com' object as third argument.
Of course, it still is wise to upgrade and benefit from all those cool
new features :)
Cheers,
Tsjerk
On
Cunliang,
There is a script available on the PyMOL-Wiki that calculates either the
center-of-mass OR the center-of-geometry.
Please see http://www.pymolwiki.org/index.php/Center_Of_Mass
It uses the pseudoatom function to generate a sphere at the desired center of
mass.
Hope this answers
Enter editing mode, select the 2 points, press Ctrl + t or type bond on the
cli.
Cheers,
Marius
On Thu, Mar 31, 2011 at 11:36 AM, kanika sharma ksharma...@gmail.comwrote:
I have two points corresponding to center of masses of 2 proteins. I have
to draw a line between both. Is there a feature
This says that bond can only be added within an object not between 2
objects.
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If I'm not mistaken, you can select both center of masses, since they
are independent objects in the right side bar, and save them together as
a single pdb. Then, when loading this single pdb, you'll be able to draw
the bond.
Hope that helps.
This says that bond can only be added within an
Hi Kanika,
You can also use pseudoatoms. If you have the positions:
pseudoatom coms,pos=[x1,y1,z1]
pseudoatom coms,pos=[x2,y2,z2]
bond coms,coms
Or, if you just have the chains:
pseudoatom coms, chain a
pseudoatom coms, chain b
bond coms, coms
Alternatively you can use CGO objects. But
Hi Kanika and Tsjerk,
if you use the commands below:
pseudoatom coms, chain a
pseudoatom coms, chain b
bond coms, coms
you create the center of geometry rather than the center of mass.
I'd like to know how to create the center of mass.
Alternatively you can use the command distance to draw a
Hi All,
I have re-written the center-of-mass script found on the Wiki (which was
actually only calculating center-of-geometry). This script provides three
improvements to the previous script: 1) The real center-of-mass can be
calculated based on a table of atomic masses, 2) pseudoatoms are
Hi all!
Two questions:
Does anyone know how to read the coordinates (x,y,z) of a selected atom
in a protein?
Or even better
Does anyone know how to visualize the center of mass of the protein,
reset the axis (x,y,z) using the centroid as origin and then calculate
the distance of a resi or an atom
Am Freitag, 2. März 2007 schrieb Filippo Marchioni:
Hi all!
Two questions:
Does anyone know how to read the coordinates (x,y,z) of a selected atom
in a protein?
Or even better
Does anyone know how to visualize the center of mass of the protein,
reset the axis (x,y,z) using the centroid as
Hi Filippo,
Here is a python script that calculates the Center of mass for a given
selection
and creates a CGO sphere there. It is is not 100% exact as it only
weighs C-Alpha atoms.
This is exactly how pymol centers selections: when you run the script,
the domain is centered and if you rotate
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